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SSRN 2022年

作者： Lou, Esther G. Sapoval, Nicolae McCall, Camille Bauhs, Lauren Carlson-Stadler, Russell Kalvapalle, Prashant Lai, Yanlai Palmer, Kyle Penn, Ryker Rich, Whitney Wolken, Madeline Ensor, Katherine B. Hopkins, Loren Treangen, Todd J. Stadler, Lauren B. Department of Civil and Environmental Engineering Rice University 6100 Main Street MS 519 HoustonTX77005 United States Department of Computer Science Rice University 6100 Main Street HoustonTX77005 United States Systems Synthetic and Physical Biology Graduate Program Rice University 6100 Main Street HoustonTX77005 United States Houston Health Department 8000 N. Stadium Dr. HoustonTX77054 United States Department of Statistics Rice University 6100 Main Street MS 138 HoustonTX77005 United States

Over the course of the COVID-19 pandemic, variants of SARS-CoV-2 have emerged that are more contagious and more likely to cause breakthrough infections. Targeted amplicon sequencing approach is a gold standard for identification and analysis of variants. However, when applied to environmental samples such as wastewater, it remains unclear how sensitive this method is for detecting variant-associated mutations in environmental samples. Here we directly compare a targeted amplicon sequencing approach (using ARTIC v3;hereafter referred to as sequencing) with RT-ddPCR quantification for the detection of five mutations that are characteristic of variants of concern (VoCs) in wastewater samples. In total, 547 wastewater samples were analyzed using both methods in parallel. When we observed positive mutation detections by RT-ddPCR, 42.6% of the detection events were missed by sequencing, due to negative detection or the limited read coverage at the mutation position. Further, when sequencing reported negative or depth-limited mutation detections, 26.7% of those events were instead positive detections by RT-ddPCR, highlighting the relatively poor sensitivity of sequencing. No or weak associations were observed between quantitative measurements of target mutations determined by RT-ddPCR and sequencing. These findings caution the use of quantitative measurements of SARS-CoV-2 variants in wastewater samples determined solely based on sequencing. © 2022, The Authors. All rights reserved.

关键词： SARS

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Application of factor analysis method to support the users acceptance model of ERP systems implementation

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Journal of Physics: Conference Series 2021年第1期1836卷

作者： W Sardjono J Sudirwan W Priatna G R Putra Information Systems Management Department BINUS Graduate Program -Master of Information Systems Management Bina Nusantara University Jakarta Indonesia – 11480 School of Information Systems Department BINUS Undergraduate Program Bina Nusantara University Jakarta Indonesia 11480 Informatics Engineering Engineering Bhayangkara University Jakarta Raya Indonesia Computer Science Study Program Faculty of Mathematics & Natural Sciences Pakuan University Bogor Indonesia

An e-Commerce company has been using an Enterprise Resource Planning (ERP) system for several years, but is still constrained in its implementation, this is reflected in the number of issue/change request tickets submitted by users who have not been able to reach ideal conditions. To overcome this problem, we need an appropriate reference model, the ERP system user acceptance model in companies. The study conducted factors that influence the level of acceptance of SAP ERP users in the XYZ group to then determine a model that is able to explain practically the level of ERP system user acceptance, which in turn can produce concrete proposals to increase ERP system user acceptance. Research is quantitative descriptive using factor analysis and regression analysis methods. The research method uses a questionnaire with a total of 107 valid respondents coming from 8 company names under the XYZ group in 6 Southeast Asian countries. The conclusion of the study is that there are 24 indicators and 4 factors that influence user acceptance of the SAP ERP system. These four factors are the low contribution of the ERP system, the quality of ERP systems and data, the development of ERP systems, and also the low quality of ERP system supporters. It is hoped that by optimizing the value of the 4 factors, the XYZ group can increase user acceptance of the SAP ERP system so that the system can provide benefits expected by the company to be competitive advantage.

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Classification of the Structural Integrity by the General Vibration Method

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Procedia computer Science 2019年 157卷 382-387页

作者： Fergyanto E. Gunawan Benfano Soewito Nico Surantha Tuga Mauritsius Nobumasa Sekishita Industrial Engineering Department BINUS Graduate Program - Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Information Systems Information Department BINUS Graduate Program - Master of Information Systems Management Bina Nusantara University Jakarta Indonesia 11480 Department of Mechanical Engineering Toyohashi University of Technology Toyohashi Aichi 441-8580 Japan

Traditionally, for the purpose of classifying the integrity of an engineering structure, one may use the information of the natural frequencies or mode shapes or some other measures derived from the two. In this research, we propose a classification method on the basis of the general vibration model. The general vibration model is essentially a set of differential equations describing the dynamics of the structure under consideration. For the purpose of damage detection, a deviation of the general vibration model from the dynamic equilibrium point marks the occurrence of the damage. To demonstrate the effectiveness of the method, we study two simplest dynamical systems consisting of one- and two-concentrated masses subjected to a prescribed dynamic load. The structural damages are introduced artificially by reducing the stiffness of spring in the structures. We find that the general vibration model is more sensitive to damages than the traditional methods.

关键词： General Vibration Model Structural Integrity Structural Health Monitoring Power Spectral Density Damage Index

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A Study of the Sensitivity of the Fuel Consumption to Driving Strategy by Micro Simulation

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Procedia computer Science 2019年 157卷 375-381页

Global warming due to excessive emission greenhouse gases is a significant issue faced by humanity, and collectively, cars and trucks contribute about 20% to the entire global-warming gases. For a reason, recently, many attempts have been endured to reduce the emission and to increase fuel efficiency, including vehicle platooning, better driving strategy, and increasing engine efficiency. This study intends to provide a more detail assessment regarding the effects of the driving strategy to fuel consumption. For the purpose, the vehicle dynamics are quantified by employing the car-following model based on the optimal velocity model. The fuel consumption is estimated from the regression model of Ahn 18 . The result suggests that the braking distance strongly affects fuel consumption.

关键词： Optimal Velocity Model Micro Simulation Car-Following Model Fuel Efficiency

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Prediction of protein subcellular localization in single cells

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Nature Methods 2025年 1-11页

作者： Zhang, Xinyi Tseo, Yitong Bai, Yunhao Chen, Fei Uhler, Caroline Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Eric and Wendy Schmidt Center Broad Institute of MIT and Harvard Cambridge MA United States Computational and Systems Biology Program Massachusetts Institute of Technology Cambridge MA United States Broad Institute of MIT and Harvard Cambridge MA United States Department of Stem Cell and Regenerative Biology Harvard University Cambridge MA United States

The subcellular localization of a protein is important for its function, and its mislocalization is linked to numerous diseases. Existing datasets capture limited pairs of proteins and cell lines, and existing protein localization prediction models either miss cell-type specificity or cannot generalize to unseen proteins. Here we present a method for Prediction of Unseen Proteins’ Subcellular localization (PUPS). PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images. We demonstrate that the protein sequence input enables generalization to unseen proteins, and the cellular image input captures single-cell variability, enabling cell-type-specific predictions. Experimental validation shows that PUPS can predict protein localization in newly performed experiments outside the Human Protein Atlas used for training. Collectively, PUPS provides a framework for predicting differential protein localization across cell lines and single cells within a cell line, including changes in protein localization driven by mutations. © The Author(s), under exclusive licence to Springer Nature America, Inc. 2025.

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Performance Analysis and Optimization of the Vector-Kronecker Product Multiplication

Performance Analysis and Optimization of the Vector-Kronecke...

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International Symposium on computer Architecture and High Performance Computing (SBAC-PAD)

作者： Alexandre Azevedo Cristiana Bentes Maria Clicia Castro Claude Tadonki Computational Sciences Program State University of Rio de Janeiro Department of Systems Engineering State University of Rio de Janeiro Department of Informatics and Computer Science State University of Rio de Janeiro CRI (Centre de Recherche en Informatique) MINES ParisTech

ISBN: (数字)9781728199245

ISBN: (纸本)9781728199252

The Kronecker product, also called tensor product, is a fundamental matrix algebra operation, used to model complex systems using structured descriptions. This operation needs to be computed efficiently, since it is a critical kernel for iterative algorithms. In this work, we focus on the vector-kronecker product operation, where we present an in-depth performance analysis of a sequential and a parallel algorithm previously proposed. Based on this analysis, we proposed three optimizations: changing the memory access pattern, reducing load imbalance and manually vectorizing some portions of the code with Intel SSE4.2 intrinsics. The obtained results show better cache usage and load balance, thus improving the performance, especially for larger matrices.

关键词： Complexity theory Optimization program processors Computational modeling Tensors Parallel algorithms Scalability

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A robotic and virtual testing platform highlighting the promise of soft wearable actuators for wrist tremor suppression

Device

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Device 2025年

作者： Alona Shagan Shomron Christina Chase-Markopoulou Johannes R. Walter Johanna Sellhorn-Timm Yitian Shao Tobias Nadler Audrey Benson Isabell Wochner Ellen H. Rumley Isabel Wurster Philipp Klocke Daniel Weiss Syn Schmitt Christoph Keplinger Daniel F.B. Haeufle Robotic Materials Department Max Planck Institute for Intelligent Systems Stuttgart Germany Institute for Modelling and Simulation of Biomechanical Systems University of Stuttgart Stuttgart Germany Stuttgart Center for Simulation Science (SimTech) University of Stuttgart Stuttgart Germany Hertie Institute for Clinical Brain Research University of Tübingen Tübingen Germany Haptic Intelligence Department Max Planck Institute for Intelligent Systems Stuttgart Germany Institute for Computer Engineering (ZITI) University of Heidelberg Heidelberg Germany Paul M. Rady Department of Mechanical Engineering University of Colorado Boulder CO USA Center for Neurology Department of Neurodegenerative Diseases University of Tübingen Tübingen Germany Center for Bionic Intelligence (BITS) Tübingen and Stuttgart Germany Material Science and Engineering Program University of Colorado Boulder CO USA Werner Reichardt Center for Integrative Neuroscience University of Tübingen Tübingen Germany

Nearly 80 million people in the world deal with medical conditions that cause involuntary periodic movements known as tremors. Wearable soft robotic devices offer a potential solution for actively suppressing these tremors. However, existing prototypes face limitations in actuation performance and complex testing procedures. We present a comprehensive approach for the rapid evaluation of emerging wearable tremor-suppression technologies. This method combines reproducing patient-recorded tremor episodes and measuring tremor suppression in a robotic platform, termed a “mechanical patient”, with validation of the achieved suppression performance of soft actuators via biomechanical modeling, thereby avoiding time-consuming clinical testing in the early stages of development. Using this approach, we highlight that an antagonistic pair of slim and lightweight electrohydraulic actuators can effectively suppress clinically relevant tremors between 2 and 8 Hz. The biomechanical model confirms that the pair of actuators generates adequate suppression forces for all tested tremors.

关键词： tremor suppression mechanical patient soft actuators wearable devices biomechanical simulation DTI-4: Validate

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A PARALLEL VARIATIONAL MESH QUALITY IMPROVEMENT METHOD FOR TETRAHEDRAL MESHES 28

A PARALLEL VARIATIONAL MESH QUALITY IMPROVEMENT METHOD FOR T...

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28th International Meshing Roundtable, IMR 2019

作者： Shontz, Suzanne M. Varilla, M.A.L. Huang, Weizhang Department of Electrical Engineering and Computer Science Bioengineering Program Information and Telecommunication Technology Center University of Kansas LawrenceKS United States Husky Injection Molding Systems Ltd. Luxembourg Luxembourg Department of Mathematics University of Kansas LawrenceKS United States

ISBN: (纸本)9781733489003

There are numerous large-scale applications requiring mesh adaptivity, e.g., computational uid dynamics and weather prediction. Parallel processing is needed for simulations involving large-scale adaptive meshes. In this paper, we propose a parallel variational mesh quality improvement algorithm for use with distributed memory machines. Our method parallelizes the serial variational mesh quality improvement method by Huang and Kamenski. Their approach is based on the use of the Moving Mesh PDE method to adapt the mesh based on the minimization of an energy functional for mesh equidistribution and alignment. This leads to a system of ordinary differential equations (ODEs) to be solved which determine where to move the interior mesh nodes. An efficient solution is obtained by solving the ODEs on subregions of the mesh with overlapped communication and computation. Strong and weak scaling experiments on up to 128 cores for meshes with up to 160M elements demonstrate excellent results. © 2019 Proceedings of the 28th International Meshing Roundtable, IMR 2019. All rights reserved.

关键词： Ordinary differential equations

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Biomedical data and AI

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Science China Life Sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Deep Learning-Derived Optimal Aviation Strategies to Control Pandemics

arXiv

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arXiv 2022年

作者： Rizvi, Syed Awasthi, Akash Peláez, Maria J. Wang, Zhihui Cristini, Vittorio Van Nguyen, Hien Dogra, Prashant Department of Electrical and Computer Engineering University of Houston HoustonTX77004 United States Mathematics in Medicine Program Department of Medicine Houston Methodist Research Institute HoustonTX77030 United States Department of Physiology and Biophysics Weill Cornell Medical College New YorkNY10065 United States Neal Cancer Center Houston Methodist Research Institute HoustonTX77030 United States Department of Imaging Physics The University of Texas M.D. Anderson Cancer Center HoustonTX77230 United States Physiology Biophysics and Systems Biology Program Graduate School of Medical Sciences Weill Cornell Medicine New YorkNY10065 United States Research in Physiology and Biophysics Department of Physiology and Biophysics Weill Cornell Medical College New YorkNY United States

The COVID-19 pandemic has affected countries across the world, demanding drastic public health policies to mitigate the spread of infection, leading to economic crisis as a collateral damage. In this work, we investigated the impact of human mobility (described via international commercial flights) on COVID-19 infection dynamics at the global scale. For this, we developed a graph neural network-based framework referred to as Dynamic Connectivity GraphSAGE (DCSAGE), which operates over spatiotemporal graphs and is well-suited for dynamically changing adjacency information. To obtain insights on the relative impact of different geographical locations, due to their associated air traffic, on the evolution of the pandemic, we conducted local sensitivity analysis on our model through node perturbation experiments. From our analyses, we identified Western Europe, North America, and Middle East as the leading geographical locations fueling the pandemic, attributed to the enormity of air traffic originating or transiting through these regions. We used these observations to identify tangible air traffic reduction strategies that can have a high impact on controlling the pandemic, with minimal interference to human mobility. Our work provides a robust deep learning-based tool to study global pandemics and is of key relevance to policy makers to take informed decisions regarding air traffic restrictions during future outbreaks. © 2022, CC BY-NC-SA.

关键词： COVID-19

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